Merge https://github.com/SimTk/openmm

platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp

@@ -24,9 +24,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceCustomTorsionIxn.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceDynamics.cpp

@@ -25,9 +25,9 @@
 #include <cstring>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceDynamics.h"
 
 #include <cstdio>

platforms/reference/src/SimTKReference/ReferenceForce.cpp

@@ -25,9 +25,9 @@
 #include <cstring>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 
 #include <cstdio>

platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceHarmonicBondIxn.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceLJCoulomb14.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp

@@ -26,9 +26,9 @@
 #include <sstream>
 #include <complex>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceLJCoulombIxn.h"
 #include "ReferenceForce.h"
 #include "PME.h"

platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp

@@ -24,9 +24,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMLog.h"
 #include "ReferenceLincsAlgorithm.h"
 #include "ReferenceDynamics.h"
 #include "openmm/OpenMMException.h"

platforms/reference/src/SimTKReference/ReferenceMonteCarloBarostat.cpp

@@ -25,7 +25,7 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceMonteCarloBarostat.h"
 
 using namespace std;

platforms/reference/src/SimTKReference/ReferencePairIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "ReferencePairIxn.h"
 

platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceProperDihedralBond.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceRbDihedralBond.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMLog.h"
 #include "ReferenceShakeAlgorithm.h"
 #include "ReferenceDynamics.h"
 #include "openmm/OpenMMException.h"

platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp

@@ -25,9 +25,9 @@
 #include <cstring>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceStochasticDynamics.h"
 #include "ReferenceVirtualSites.h"
 

platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp

@@ -25,9 +25,9 @@
 #include <cstring>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceVariableStochasticDynamics.h"
 #include "ReferenceVirtualSites.h"
 

platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceVariableVerletDynamics.h"
 #include "ReferenceVirtualSites.h"
 

platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp

@@ -25,9 +25,9 @@
 #include <cstring>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceVerletDynamics.h"
 #include "ReferenceVirtualSites.h"
 

platforms/reference/src/gbsa/CpuGBVI.cpp

@@ -26,8 +26,8 @@
 #include <sstream>
 #include <stdio.h>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKReference/ReferenceForce.h"
+#include "SimTKOpenMMCommon.h"
+#include "ReferenceForce.h"
 #include "CpuGBVI.h"
 
 using namespace std;

platforms/reference/src/gbsa/CpuObc.cpp

@@ -28,8 +28,8 @@
 #include <cmath>
 #include <cstdio>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKReference/ReferenceForce.h"
+#include "SimTKOpenMMCommon.h"
+#include "ReferenceForce.h"
 #include "CpuObc.h"
 
 using namespace OpenMM;

platforms/reference/src/gbsa/GBVIParameters.cpp

@@ -28,7 +28,7 @@
 
 #include "openmm/OpenMMException.h"
 #include "GBVIParameters.h"
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "SimTKOpenMMCommon.h"
 
 using std::vector;
 using OpenMM::RealVec;

platforms/reference/src/gbsa/ObcParameters.cpp

@@ -28,7 +28,7 @@
 
 #include "openmm/OpenMMException.h"
 #include "ObcParameters.h"
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "SimTKOpenMMCommon.h"
 
 using std::vector;